This was using a project imported from an earlier version. In 7.1 I created a templates directory in the WEB-INF directory in the projects tab to store facelet templates to protect them against direct access according to good practice. However when loading the same project in this latest dev build, the directory does not appear to exist in the project, but when the project is run, the pages work; meaning the files are really there but Netbeans is not showing them. I think this is a significant bug for anyone upgrading.
I'm including screen shots of what the WEB-INF directory looks like in both version 7.1 and in this latest dev build. Also note that the directories don't even appear in the files tab.
Note that this dev version does show improvement as it actually succeeds in running this project (i.e. deploys and runs in glassfish) while base 7.2 does not per Bug 214198 (and while 7.1 has no issues with it at all). Glad to see the good work and effort.
Product Version = NetBeans IDE Dev (Build 201209020001)
Operating System = Linux version 3.2.0-29-generic (Kubuntu 12.04) running on amd64 (i7 920)
Java; VM; Vendor = 1.7.0_05
Runtime = Java HotSpot(TM) 64-Bit Server VM 23.1-b03

Created attachment 123842[details]
Project on Disk showing web-inf in v7.1 with all sub folders correct
Project was created in v7.1. In the web-inf folder a facelettemplates folder was created to hold template files. This directory of course shows up fine in 7.1. Here is a screen shot showing this as a comparison to the next screen shot (to be attached) where it does not exist in the new build.

Created attachment 123843[details]
Project on Disk missing web-inf subfolders in dev build associated with this bug
The facelettemplates folder is missing from the web-inf folder in the IDE (they are there on the disk). The project runs, but I can't manage the project like this.

RE. "Also note that the directories don't even appear in the files tab." - this indicates that this is NB FileSystem API issue. Web Project's "Web Pages" node is just a delegate to underlying DataFolder and does not filtering.
Btw. do you use any versioning control?